Intro to Virology

• Complete Protein synthesis machinery

• Obligate intercellular (no gene to encode proteins involved in energy production and membrane biosynthesis)

• Resistant to antibiotics!

• *Inhibited by” Interferon and antiviral agents

  • Interferon: proteins part of natural defeses; interferes with viruses and keeps them from multiplying; activated IFN gene

• * The only taxa used in classifying viruses: Order, Suborder, Family, Subfamily, Genus, Subgenus, and Species.

  • Missing: Domain, Kingdom, Phylum, Class

  • Order: Virales

  • Family: Viridae

  • Subfamily: Virinae

  • Genus: Virus

  • Species (generally the desease virus): e.g. SARS COvv2, Varicella zoster virus, measles virus

• What do you call an entire infectious unit? VIRION

• What are the 2 types of Virions?

  • Naked nucleocapsid virions

    • capsid covering

    • nucleic acid genome

  • Enveloped virions

    • Capsid covering

    • Nucleic acid genome

    • *ENVELOPE - protruding spike on its surface

      • Phospholipid bilayer

      • contains inserted Viral proteins called PEPLOMERS

        • For attachment, induction of productive immunity

        • Hemagglutinin (HA) = Attachment of virus to RBC receptor (specifically the glycan chain)

        • Neuramidase (NA)

        • Spike protein = attach to ACE2 receptor (in SARCOV1 and SARVOC2)

          • specific binding ; facillitate viral entry; made up of Glycoproteins

          • E.g. Gp 120 spikes (attaches to CD4+ receptor of host cell)

            • *HIV patients have decreased CD4+ receptor.

            • Coreceptors of Gp 120 spike: CCR5 and CXCR 4

• Derived from host cell membrane during Cell maturation

  • NOTE: except herpes, its envelope is derived from the nuclear membrane.

• Majority of human viruses are ENVELOPED EXCEPT:

  • Parvoviridae

  • Papillomaviridae

  • Polyomaviridae

  • Adenoviridae

  • Picornaviridae

  • Reoviridae

  • Calciviridae

  • Hepeviridae

RNA VIRUSES

Image Above^

• take note of types and examples:

  • Double stranded RNA (DsRNA)

  • Single stranded Negative strand RNA (ssRNA-)

  • Single stranded Positive strand RNA (ssRNA+)

  • Single stranded Single RNA Retrovirus (RT)

DNA VIRUSES

Image Above^

• take note of types and examples:

  • Double stranded DNA (dsDNA)

  • Single stranded POSITIVE DNA (ssDNA+)

  • dsDNA (RT)

Capsid ( 3 types according to symmetry)

1. Icosahedral

2. Helical

3. Complex

* Icosahedral and Helical have enveloped and naked.

Icosahedral

• 20 flat sides

• DNA

• (+) sense strand RNA

Helical

• (-) sense strand RNA

Complex

• No symmetrical features

• E.g. Pox and Rabies

  • Pox = dumbbell shaped

  • Rabies = bullet shaped

Kaposis Sarcoma ass. herpes virus ( KSHV or Herpesvirus 8)

• Spike proteins: gB & gHgL

• Human receptor: CD98

Summary of Viral proteins and their functions

• Function of RNA polymerase? helps viral transduction, translation and replication

• Function of RNA transcriptase? 1) Found in retroviruses 2) Make DNA copy of viral RNA

• Matrix protein is found inbetween?

• Viral antigens of Hepatitis B?

  • HBsAg (acute)

  • HBcAg (chronic)

  • HBeAg

• How do determine antigens of Hep B? check antibodies produced by PTs

Genome

• Strands

  • Linear: Pico, Pox, Parvo

  • Circular:

    • single: Herpes D

    • double: Papillomavirus **

      

  • Segmented: “B-O-A-R”

    • orthomyxoviridae

    • Arenaviridae

    • Bunyviridae

    • Reovirus **

      

      
      

MUST REMEMBERS

• ALL DNA VIRUSES ARE: linear & DS

  • EXCEPT: ssDNA (Parvoviridae) & Circular DNA (Papilloviridae, Polyomaviridae, Hepadnaviridae)

• DS DNA VIRUSES HAVE BOTH: (+) and (-) strand

  • IF SS? only (+) strand!!!!! ***

• ALL RNA VIRUSES ARE: linear and SS

  • EXCEPT: BOAR

    • dsRNA (Reoviridae)

    • ssRNA segmented genomes (Orthomyxoviridae, Bunyaviridae, Arenaviridae)

    • Circular RNA (Delta virus)

• SS RNA only have: (-) strand

  • must transcribe first (-) then (+) strand

  • own RNA dependent polymerase **

  • memorize: Negative strand RNA viruses

    • Always Bring Polymerase Or Fail Replication

      • Arena

      • Bunya

      • Paramyxo

      • Filo

      • Rhabdo

    • mRNA polarity matches the host cell = (-) to (-)

Polarity

Viral RNA Polarity describes whether a viral single-stranded RNA genome can be read directly by host ribosomes to make protein, or if it must be converted first.

1. Positive-Sense (+) ssRNA

• Mechanism: The viral RNA strand is identical in polarity to host mRNA ("sense" strand).

• Process: Host ribosomes directly bind the viral genome and translate it immediately into viral proteins (+ RNA → Protein).

• Key Feature: Pure, naked (+) RNA is infectious on its own because it requires no pre-packaged viral enzymes to begin protein synthesis.

• Examples: Picornavirus, Togavirus, Coronavirus (Baltimore Group IV).

2. Negative-Sense (−) ssRNA

• Mechanism: The viral RNA strand is complementary (antisense) to host mRNA. Ribosomes cannot read it.

• Process: The virus brings its own pre-packaged enzyme, RNA-dependent RNA polymerase (RdRP). This polymerase uses the (-) strand as a template to transcribe (+) viral mRNA, which the host ribosome then translates (- RNA → + mRNA → Protein).

• Key Feature: Naked (−) RNA is not infectious alone because human host cells do not possess an RdRP enzyme.

• Examples: Rhabdovirus, Orthomyxovirus (Baltimore Group V).

3. Ambisense (+ and −)

• Mechanism: A single RNA segment contains both (+) sense and (−) sense coding regions on the same strand.

• Composition: The genome is mostly composed of (−) polarity regions interspersed with (+) polarity regions.

• Process: The (+) portion and (−) portion are transcribed and translated at different stages of the viral replication cycle, typically requiring the viral RdRP.

• Examples: Arenaviridae (Lassa fever virus) and Bunyaviridae (Hantavirus).

Baltimore classification groups

I. Group 1 dsDNA

• Direct central dogma; follows conventional host pathway

  • dsDNA → mRNA → Protein

  • NO reverse transcriptase or intermediate RNA steps

• Enzyme for protein expression: DNA-dependent RNA polymerase

  • transcribes DNA template directly into (+) viral mRNA

• Enzyme for Genome replication: DNA-dependent RNA polymerase  

  • duplicates BOTH (+) and (-) strands

• Cellular compatibility

  • same double stranded format as host genome

  • same polarity as host genome

• Classic Examples (Clinical High-Yield): Herpesviridae, Adenoviridae, Papillomaviridae, Polyomaviridae, and Poxviridae (Poxvirus replicates exceptionally in the cytoplasm using its own carried enzymes)

II. Group 2 ssDNA

• Mostly (+) polarity

• Cannot transcribe directly!

  • Host RNA polymerase can only recognize dsDNA templates

$\text{ssDNA} \xrightarrow{\text{Host DNA Pol}} \text{dsDNA intermediate} \xrightarrow{\text{Host RNA Pol}} \text{mRNA} \longrightarrow \text{Protein}$

• High-Yield Medical Example!

  • Parvoviridae (Parvovirus B19):

    • Smallest DNA virus.

    • Non-enveloped, icosahedral capsid.

    • Clinically causes Erythema infectiosum (Fifth disease / "slapped-cheek" rash) in children, aplastic crisis in patients with sickle cell/chronic hemolytic anemia, and hydrops fetalis in pregnant women.

III. Group 3 dsRNA (+ and -)

• Only 1 Family

  • Reoviridae (e.g., Rotavirus – common cause of infantile diarrhea, non-enveloped, segmented genome, triple-layered capsid).

• Cannot Translate Directly

  • The (+) strand is hydrogen-bonded to the (−) strand, so it cannot act directly as mRNA.

• Key Enzyme: own RNA-dependent RNA polymerase (RdRP)

  • Acts as both a transcriptase (transcribes (−) strand into (+) mRNA) and a replicase (copies both strands to reproduce dsRNA).

IV. Group 4: (+) ssRNA

• Direct Translation: The genome acts directly as mRNA and is translated immediately upon entry by host ribosomes.

• Infectious Genome: Pure, naked (+) ssRNA is infectious on its own.

• Replication Cycle:

  1. Translates viral RdRP (replicase) first.

  2. Uses (+) strand to make a (−) ssRNA intermediate.

  3. Uses the (−) template to generate new (+) ssRNA strands.

• Examples: Caliciviridae (Norwalk), Coronaviridae (SARS, MERS), Hepeviridae (Hepatitis E), Picornaviridae (Polio), Togaviridae (Rubella), Flaviviridae (Dengue).

V. Group 4: (−) ssRNA

• Not Directly Readable / Not Infectious Alone: Cannot be translated by host ribosomes; naked RNA is non-infectious.

• Must Pre-Package Enzyme: Virion must carry RdRP inside its capsid.

• Replication Cycle:

  1. RNA dependent RNA Polymerase (RdRP) transcribes (−) ssRNA into (+) mRNA → translated to protein.

  2. RdRP synthesizes a (+) ssRNA template intermediate to replicate new (−) ssRNA genomes.

• Mnemonic ("Always Bring Polymerase Or Fail Replication"):

  • Arenaviruses (Lassa fever)

  • Bunyaviruses (Hantaan virus)

  • Paramyxoviruses (Mumps, Measles)

  • Orthomyxoviruses (Influenza)

  • Filoviruses (Ebola, Marburg)

  • Rhabdoviruses (Rabies)

  • Delta virus (Hepatitis D – subviral agent under Group V)

VI. Group 6: (+) ssRNA Retroviruses

• Unique Pathway: Despite having (+) ssRNA, it is NOT used directly as mRNA.

• Key Enzymes:

  • Reverse Transcriptase (RNA-dependent DNA polymerase)

    • Transcribes (+) ssRNA → ssDNA → dsDNA.

  • Integrase

    • Integrates viral dsDNA (provirus) into the host cell chromosomes.

• Protein Synthesis: Host RNA polymerase transcribes integrated proviral DNA into mRNA.

• Examples: Retroviridae (HIV, HTLV; enveloped, icosahedral, replicates in nucleus).

VII. Group 7: dsDNA (+/−) "Gapped DNA" Retrovirus

• Structure: Circular, partially double-stranded "gapped" DNA (segments of single-stranded DNA).

• Replication Intermediate

  • Replicates via an ssRNA intermediate (pregenomic RNA) using reverse transcriptase to convert RNA back into gapped dsDNA.

• Example: Hepadnaviridae (Hepatitis B; enveloped, icosahedral, replicates in nucleus).

Viral Replication Cycle

• MEMORIZE: “APUSAR”

  • Attachment - via capsid or phospholipid envelope (i.e. Spikes)

  • Penetration

    • Direct Fusion w/ host cell membrane

    • Viroprexis (receptor mediated endocytosis) ; used by several enveloped and ALL NAKED viruses

  • Uncoating - degredation or removal of capsid = release of nucleic acid/ genome

    • Start of Eclipse Phase in the Viral Growth curve (?)

      • Period when the infectious particles cannot be recovered from the collected

        specimen

  • Synthesis

    • DNA viruses replicates in the nucleus

      → Except: poxviruses

    • RNA viruses replicates in the cytoplasm

      → Except: Orthomyxoviruses (influenza) & Retroviruses (HIV, HTLV, Hep B)

    •  Production of nucleic acid and protein polymers

  • Assembly

    • structural proteins, genomes and viral enzymes are assembled into virus particles

    • Enclosing of the viral genome in protein coat (capsid)

  • Release

    • Last step of replication cycle

    • Released through:

      • Budding: creating enveloped viruses from the host cell membrane

    • Lysis: most naked viruses

      • Can sometimes result to APOPTOSIS: release by lysis of naked viruses results in host cell death

Viral Growth Curve

Phase 0: Entry

Phase1:Decline

→ Virus decreases in number but continues to function

Phase 2: Eclipse Period

→ No virus is detectable inside the cell
→ Viral component synthesis occurs
→ Virus are preparing by synthesizing their proteins and genome

Phase 3: Exponential/Rise Period
→ Period where they replicate exponentially
→ Progeny virus increases exponentially for a period of time (8-72 hours)

Phase 4: Latent Period

→ No additional increase in virus yield occurs

•  After reaching their certain number, there is plateau where there is no additional viruses

→  May yield of 100-10,000 virions per cell

→  Can be intracellular or extracellular

• When released extracellularly, they try to look for other host cell to infect

Phase 5: CytoplasmicEffect

→  Mark derangement of cell function leading to lysis and cell death ▪ Changes in cell size and shape (elongation, ballooning)
    ▪  Can sometimes lead to cell lysis or death of the infected host cell

→  Virus replicate and produce progeny

→  Nucleic acid synthesis leading to host cell death and cytopathic effects

(CPE)

→  Inhibition of cellular protein and nitric acid (NA) synthesis

Patterns of Viral Infections & Cytopathology

1. Abortive

   • e.g. Hepatitis D (cannot replicate w/o Hepatitis B)

   • Aka Viruzoid or Satellite

2. Lytic

   • Virus replicates and produce Progeny

   • Leads to cell death and Cytopathic effects (CPE)

   • Inhibits cellular protein and nucleic acid synthesis

   • Evidence:

     • Thickening / Swelling

     • Presence of Inclusion bodies

     • Syncytial bodies (cell fusion of infected Host cell)

       

3. Persistent

   • Small # of virus particles are produced w/ little to no CPE

   • infected cells survice the effects of viral replication

   • 3 types:

     • viral transformation → caused by oncogenic viruses

     • chronic infection → low level or viral production w/o immune clearance (e.g. Hep B or C)

     • latent infection → Viral genetic material remain in host cell, activated in the later time.

Types of Culture for Viruses

• which one is used for vaccine production? Primary culture

• which one is transfered from primary cells and is also used for vaccine prodcution? Semicontinuous culture

• Which one is used for the production of serologic antigens (e.g. HeLa culture)? Continuous culture

• What is used to detect specific nucleic acids in viruses? PCR

• What 3 processes happens during PCR? D-A-E; Denaturing, Annealing and Extending

Development of Cytopathic Effects (CPE)

1. Syncytial formation

2. Ballooning of cells

Syncytial formation (or a Multi-nucleated enlarged cell)

• Middle cell with the infected virus fuses with neighboring cell to produce syncytium.

• E.g. Respiratory Virus (RSV) and Measles Virus

Balloon Formation

• Original shape of cell is not present anymore ; Infected cell becomes round/balloon

• E.g. Enterovirus and HSV

*Viral growth in Chick Embryo detects the presence of? (1) Pocks on CAM (2) Hemagglutination (3) Inclusion bodies (negribodies)